I was wondering how I might be able to use the BioPython package to extract nucleotide frequencies over an aligned set of sequences. Does anybody know how I might be able to do this? I am assuming that I have aligned sequences, including the appropriate spacers at places where base pair deletions have occurred.

Is there a single function in the BioPython package that allows me to do that? I've tried browsing through the API, but I haven't been able to find anything. (It might be I'm not looking at it correctly, or that the terminology used is different, perhaps?)

I was trying to do the same thing recently, and like you couldn't find anything. In the end I used pycogent which has quite a rich API for alignments. Take a look at this page for some toy examples of doing this.